{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T11:26:59Z","timestamp":1773660419145,"version":"3.50.1"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2020,2,12]],"date-time":"2020-02-12T00:00:00Z","timestamp":1581465600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007618","type":"journal-article","created":{"date-parts":[[2020,2,12]],"date-time":"2020-02-12T13:24:25Z","timestamp":1581513865000},"page":"e1007618","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":22,"title":["A stochastic model for simulating ribosome kinetics in vivo"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8344-8446","authenticated-orcid":true,"given":"Eric Charles","family":"Dykeman","sequence":"first","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,2,12]]},"reference":[{"issue":"19","key":"pcbi.1007618.ref001","first-page":"9031","article-title":"Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution","volume":"44","author":"H Zur","year":"2016","journal-title":"Nucleic acids research"},{"issue":"20","key":"pcbi.1007618.ref002","doi-asserted-by":"crossref","first-page":"10098","DOI":"10.1093\/nar\/gks825","article-title":"The architecture of eukaryotic translation","volume":"40","author":"D Chu","year":"2012","journal-title":"Nucleic acids research"},{"issue":"2","key":"pcbi.1007618.ref003","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1093\/bioinformatics\/btr650","article-title":"A novel and versatile computational tool to model translation","volume":"28","author":"D Chu","year":"2011","journal-title":"Bioinformatics"},{"issue":"9","key":"pcbi.1007618.ref004","doi-asserted-by":"crossref","first-page":"2120","DOI":"10.1016\/j.bpj.2016.04.004","article-title":"Analysis of translation elongation dynamics in the context of an Escherichia coli cell","volume":"110","author":"JP Vieira","year":"2016","journal-title":"Biophysical journal"},{"issue":"1","key":"pcbi.1007618.ref005","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/bip.1968.360060102","article-title":"Kinetics of biopolymerization on nucleic acid templates","volume":"6","author":"CT MacDonald","year":"1968","journal-title":"Biopolymers: Original Research on Biomolecules"},{"issue":"5","key":"pcbi.1007618.ref006","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1002\/bip.1969.360070508","article-title":"Concerning the kinetics of polypeptide synthesis on polyribosomes","volume":"7","author":"CT MacDonald","year":"1969","journal-title":"Biopolymers: Original Research on Biomolecules"},{"issue":"1","key":"pcbi.1007618.ref007","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/0301-4622(74)80026-8","article-title":"On some stochastic models for protein biosynthesis","volume":"2","author":"J Hiernaux","year":"1974","journal-title":"Biophysical chemistry"},{"issue":"2","key":"pcbi.1007618.ref008","doi-asserted-by":"crossref","first-page":"021910","DOI":"10.1103\/PhysRevE.68.021910","article-title":"Totally asymmetric exclusion process with extended objects: a model for protein synthesis","volume":"68","author":"LB Shaw","year":"2003","journal-title":"Physical Review E"},{"issue":"9","key":"pcbi.1007618.ref009","doi-asserted-by":"crossref","first-page":"e1002127","DOI":"10.1371\/journal.pcbi.1002127","article-title":"Genome-scale analysis of translation elongation with a ribosome flow model","volume":"7","author":"S Reuveni","year":"2011","journal-title":"PLoS computational biology"},{"issue":"1","key":"pcbi.1007618.ref010","doi-asserted-by":"crossref","first-page":"e201204002","DOI":"10.5936\/csbj.201204002","article-title":"Mathematical and computational modelling of ribosomal movement and protein synthesis: an overview","volume":"1","author":"T von der Haar","year":"2012","journal-title":"Computational and Structural Biotechnology Journal"},{"issue":"9","key":"pcbi.1007618.ref011","doi-asserted-by":"crossref","first-page":"e1001128","DOI":"10.1371\/journal.pgen.1001128","article-title":"Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias","volume":"6","author":"P Shah","year":"2010","journal-title":"PLoS genetics"},{"issue":"2","key":"pcbi.1007618.ref012","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.cell.2010.02.036","article-title":"A role for codon order in translation dynamics","volume":"141","author":"G Cannarozzi","year":"2010","journal-title":"Cell"},{"issue":"30","key":"pcbi.1007618.ref013","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1098\/rsif.2008.0221","article-title":"Control of translation initiation: a model-based analysis from limited experimental data","volume":"6","author":"RJ Dimelow","year":"2008","journal-title":"Journal of the Royal Society Interface"},{"issue":"1","key":"pcbi.1007618.ref014","doi-asserted-by":"crossref","first-page":"011142","DOI":"10.1103\/PhysRevE.85.011142","article-title":"Mixed population of competing totally asymmetric simple exclusion processes with a shared reservoir of particles","volume":"85","author":"P Greulich","year":"2012","journal-title":"Physical Review E"},{"issue":"8","key":"pcbi.1007618.ref015","doi-asserted-by":"crossref","first-page":"E1336","DOI":"10.1073\/pnas.1615351114","article-title":"Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling","volume":"114","author":"T Matsuura","year":"2017","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"2","key":"pcbi.1007618.ref016","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/jbiol24","article-title":"Guanine-nucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs","volume":"4","author":"AV Zavialov","year":"2005","journal-title":"Journal of biology"},{"issue":"37","key":"pcbi.1007618.ref017","doi-asserted-by":"crossref","first-page":"13670","DOI":"10.1073\/pnas.0606099103","article-title":"Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome","volume":"103","author":"B Wilden","year":"2006","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"9","key":"pcbi.1007618.ref018","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1016\/j.jmb.2015.01.007","article-title":"On the pH dependence of class-1 RF-dependent termination of mRNA translation","volume":"427","author":"G Indrisiunaite","year":"2015","journal-title":"Journal of molecular biology"},{"issue":"2","key":"pcbi.1007618.ref019","first-page":"1553","article-title":"Modulation of chemical composition and other parameters of the cell by growth rate","volume":"2","author":"H Bremer","year":"1996","journal-title":"Escherichia coli and Salmonella: cellular and molecular biology"},{"issue":"25","key":"pcbi.1007618.ref020","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions","volume":"81","author":"DT Gillespie","year":"1977","journal-title":"The journal of physical chemistry"},{"issue":"12","key":"pcbi.1007618.ref021","doi-asserted-by":"crossref","first-page":"5708","DOI":"10.1093\/nar\/gkv480","article-title":"An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update","volume":"43","author":"EC Dykeman","year":"2015","journal-title":"Nucleic acids research"},{"issue":"9","key":"pcbi.1007618.ref022","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1063\/1.1778376","article-title":"Efficient formulation of the stochastic simulation algorithm for chemically reacting systems","volume":"121","author":"Y Cao","year":"2004","journal-title":"The journal of chemical physics"},{"issue":"6","key":"pcbi.1007618.ref023","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/ng.821","article-title":"General properties of transcriptional time series in Escherichia coli","volume":"43","author":"Lh So","year":"2011","journal-title":"Nature genetics"},{"issue":"11","key":"pcbi.1007618.ref024","doi-asserted-by":"crossref","first-page":"3037","DOI":"10.1128\/JB.182.11.3037-3044.2000","article-title":"mRNA composition and control of bacterial gene expression","volume":"182","author":"ST Liang","year":"2000","journal-title":"Journal of bacteriology"},{"issue":"10","key":"pcbi.1007618.ref025","doi-asserted-by":"crossref","first-page":"e1003909","DOI":"10.1371\/journal.pcbi.1003909","article-title":"Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro","volume":"10","author":"S Rudorf","year":"2014","journal-title":"PLoS computational biology"},{"issue":"5","key":"pcbi.1007618.ref026","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1006\/jmbi.1996.0428","article-title":"Co-variation of trna abundance and codon usage inescherichia coliat different growth rates","volume":"260","author":"H Dong","year":"1996","journal-title":"Journal of molecular biology"},{"issue":"1","key":"pcbi.1007618.ref027","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/0092-8674(78)90312-4","article-title":"Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates","volume":"14","author":"S Pedersen","year":"1978","journal-title":"Cell"},{"issue":"8","key":"pcbi.1007618.ref028","doi-asserted-by":"crossref","first-page":"e0134994","DOI":"10.1371\/journal.pone.0134994","article-title":"Protein synthesis in E. coli: dependence of codon-specific elongation on tRNA concentration and codon usage","volume":"10","author":"S Rudorf","year":"2015","journal-title":"PloS one"},{"issue":"3","key":"pcbi.1007618.ref029","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1529\/biophysj.106.087825","article-title":"A model for protein translation: polysome self-organization leads to maximum protein synthesis rates","volume":"92","author":"H Zouridis","year":"2007","journal-title":"Biophysical journal"},{"issue":"8","key":"pcbi.1007618.ref030","doi-asserted-by":"crossref","first-page":"e1006979","DOI":"10.1371\/journal.pcbi.1006979","article-title":"Efficiency of protein synthesis inhibition depends on tRNA and codon compositions","volume":"15","author":"S Rudorf","year":"2019","journal-title":"PLoS computational biology"},{"issue":"3","key":"pcbi.1007618.ref031","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/0022-2836(87)90180-X","article-title":"Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene","volume":"195","author":"B Berkhout","year":"1987","journal-title":"Journal of molecular biology"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007618","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,2,12]],"date-time":"2020-02-12T13:25:08Z","timestamp":1581513908000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007618"}},"subtitle":[],"editor":[{"given":"Attila","family":"Csik\u00e1sz-Nagy","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,2,12]]},"references-count":31,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2020,2,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007618","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,2,12]]}}}